vibesketch.chem.analysis

Elemental analysis and calculated descriptors of a species (#93).

The elemental analysis is exact arithmetic on the formula: each element’s share of the molar mass, with RDKit’s standard atomic weights and an isotope label’s own mass. The analysis line is in the ACS style for combustion (CHNS) analysis, “Anal. Calcd for C9H8O4: C, 60.00; H, 4.48.”, ACS Guide to Scholarly Communication, “Elemental analysis”: https://pubs.acs.org/doi/book/10.1021/acsguide

The descriptors are RDKit’s, and they are estimates, not measurements:

• logP and molar refractivity: atom contributions of S. A. Wildman and G. M. Crippen, J. Chem. Inf. Comput. Sci. 39 (1999) 868-873, doi:10.1021/ci990307l (Crippen.MolLogP, Crippen.MolMR);

• topological polar surface area: P. Ertl, B. Rohde and P. Selzer, J. Med. Chem. 43 (2000) 3714-3717, doi:10.1021/jm000942e (rdMolDescriptors.CalcTPSA, N and O only);

• hydrogen-bond donors and acceptors in Lipinski’s counting, C. A. Lipinski et al., Adv. Drug Delivery Rev. 23 (1997) 3-25, doi:10.1016/S0169-409X(96)00423-1 (CalcNumLipinskiHBD/HBA);

• rotatable bonds, heavy atoms and rings (SSSR) as RDKit counts them.

Module Attributes

COMBUSTION

The elements a combustion analysis reports, in the order the line gives them.

Functions

descriptors(mol)	Crippen logP and molar refractivity, TPSA, Lipinski donors and acceptors, counts.
elemental_analysis(mol)	The mass percent of each element of mol, implicit hydrogens included.

Classes

Analysis(formula, mass_percent, line)	Mass percent per element in Hill order, and the formatted analysis line.
Descriptors(logp, molar_refractivity, tpsa, ...)	Calculated estimates: RDKit's values, unrounded.

class vibesketch.chem.analysis.Analysis(formula, mass_percent, line)

Bases: object

Mass percent per element in Hill order, and the formatted analysis line.

Parameters:

• formula (str)

• mass_percent (dict[str, float])

• line (str)

formula: str

mass_percent: dict[str, float]

line: str

to_dict()

Return type:

dict[str, Any]

class vibesketch.chem.analysis.Descriptors(logp, molar_refractivity, tpsa, hbond_donors, hbond_acceptors, rotatable_bonds, heavy_atoms, rings)

Bases: object

Calculated estimates: RDKit’s values, unrounded.

Parameters:

• logp (float)

• molar_refractivity (float)

• tpsa (float)

• hbond_donors (int)

• hbond_acceptors (int)

• rotatable_bonds (int)

• heavy_atoms (int)

• rings (int)

logp: float

molar_refractivity: float

tpsa: float

hbond_donors: int

hbond_acceptors: int

rotatable_bonds: int

heavy_atoms: int

rings: int

to_dict()

Return type:

dict[str, Any]

vibesketch.chem.analysis.descriptors(mol)

Crippen logP and molar refractivity, TPSA, Lipinski donors and acceptors, counts.

Parameters:

mol (Any)

Return type:

Descriptors

vibesketch.chem.analysis.elemental_analysis(mol)

The mass percent of each element of mol, implicit hydrogens included.

Parameters:

mol (Any)

Return type:

Analysis